[BioRuby] Bio::Ensembl#exportview => timeout when behind proxy server

[Mitsuteru Nakao]

Hi jan,

I updated ensembl.rb.
Now, you can use a proxy server by 'http_proxy' environment variable
(like the open-uri manner).

Thanks Goto-san for his quick hack of
Bio::Command::NetTools.net_http_start method.


> I'm testing out the Bio::Ensembl file, and seem to bump into a wall that
> becomes pretty well-known to me: I'm behind a proxy server. When I try
> to run the code
>   Bio::Ensembl::Human.exportview(1,12345,22345)
> I get a timeout on the line in bio/io/ensembl.rb containing
>   cgi.exec(@hash.update(opts))
>
> Apparently, there is no option yet in the Bio::Ensembl::Base::Client
> class to give a proxy-server and proxy-address yet. Or if there _is_,
> it's not clear to me how to set these two arguments.
> I don't know if open-uri would be a solution to this, or not.

Best,
Mitsuteru
-
Mitsuteru NAKAO, Ph.D.
n at bioruby.org